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Add --call-region to Manta command #78

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Faizal-Eeman opened this issue Oct 25, 2022 · 3 comments
Open

Add --call-region to Manta command #78

Faizal-Eeman opened this issue Oct 25, 2022 · 3 comments
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@Faizal-Eeman
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enhancement New feature or request

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@Faizal-Eeman
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    I think you should add the `--call-region` option or leave an extra option here. `--call-region` will reduce the run time a lot in real data. I have a related discussion in `call-sSNV` [here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/76)

Originally posted by @maotian06 in #74 (comment)
@Faizal-Eeman Faizal-Eeman self-assigned this Oct 25, 2022
@rhughwhite
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Related to this, I'd like to use the --exome option at some stage. https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#exometargeted

@Faizal-Eeman Faizal-Eeman added the enhancement New feature or request label Feb 7, 2023
@Faizal-Eeman
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Interesting! We can look into this.

@rhughwhite
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@maotian06 pointed out to me that call-sSNV runs manta as part of strelka2 and can accept the --exome option (outputs are considered intermediate files). Planning to try this out.

@rhughwhite rhughwhite mentioned this issue Feb 9, 2023
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@Faizal-Eeman Faizal-Eeman

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@rhughwhite @Faizal-Eeman